BLASTP 2.2.18 [Mar-02-2008]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 0025.0137.p
         (431 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311231|ref|YP_003775323.1| recombination factor RarA prote...   624   e-180

>gi|300311231|ref|YP_003775323.1| recombination factor RarA protein
           [Herbaspirillum seropedicae SmR1]
          Length = 434

 Score =  624 bits (1609), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 311/426 (73%), Positives = 343/426 (80%), Gaps = 1/426 (0%)

Query: 3   SAPLAERLRPHSFDDVIGQQHLLGAGKPLRVAFESGEPHSMILWGPPGVGKTTLARIMAD 62
           +APLAE LRP + D+VIGQ HLLG GKPLR+AF+SG+PHSMI WGPPGVGKTTLAR+ A 
Sbjct: 10  AAPLAEALRPKTLDEVIGQSHLLGEGKPLRLAFQSGKPHSMIFWGPPGVGKTTLARLTAT 69

Query: 63  SFNAEFIALSAVLSGVKDIREAVERAEVIRANSGRRTILFVDEVHRFNKSQQDAFLPHVE 122
           +F  EFIALSAV SGVKDIR A+E+AE   A  G+ TILFVDE+HRFNKSQQDA LP+ E
Sbjct: 70  AFECEFIALSAVFSGVKDIRAAMEQAEQNLA-MGKHTILFVDEIHRFNKSQQDALLPYAE 128

Query: 123 SGLFTFIGATTENPSFEVNGALLSRAAVYVLKSLTEEDLGALIDRACRDELDGLQFVPEA 182
           SGL TFIGATTENPSFEVN ALLSRA VYVLKSLT+E+L  L+ RA    L  LQF  +A
Sbjct: 129 SGLVTFIGATTENPSFEVNSALLSRAQVYVLKSLTDEELKQLLKRAQDKALGDLQFDQQA 188

Query: 183 REMLIASADGDGRKLLNNLEIVARAAQAKSVAIVGTELLAECLGDALRRFDKGGDAFYDQ 242
            + +I  ADGD R+ LN LE    AA+     +V  E L   L    RRFDKGGD FYDQ
Sbjct: 189 TDTIIGYADGDARRFLNLLEQTDTAARTTGTRLVTAEFLQNALTLNSRRFDKGGDNFYDQ 248

Query: 243 ISALHKSVRGSSPDGALYWLTRMLDGGTDPRYLARRIVRMAWEDIGLADPRAMTIANDAA 302
           ISALHKSVRGS PD ALYWLTRMLDGG DPRYL+RRIVRMAWEDIGLADPRAM IANDAA
Sbjct: 249 ISALHKSVRGSHPDAALYWLTRMLDGGADPRYLSRRIVRMAWEDIGLADPRAMQIANDAA 308

Query: 303 ATYERLGSPEGELALAQAVIYLAIAAKSNAGYMAYNQARAFVAKDKSRGVPEHLRNAPTK 362
            TYERLGSPEGELAL QAVIYLA+AAKSNAGY AYN ARAFV +DKSR VP HLRNAPTK
Sbjct: 309 LTYERLGSPEGELALGQAVIYLAVAAKSNAGYNAYNAARAFVKQDKSREVPVHLRNAPTK 368

Query: 363 LMKQLGYGKLYRYAHDEPEGYAAGETYLPDGIPDPHWYQPVPRGLEAKIGDKMAHLRELD 422
           LMK+LGYG  YRYAHDEP  YAAGETYLPDGI +P WYQPVPRGLE KIG+K+A LR+ D
Sbjct: 369 LMKELGYGHEYRYAHDEPNAYAAGETYLPDGIEEPGWYQPVPRGLEIKIGEKLATLRQWD 428

Query: 423 REYKKN 428
            E +K+
Sbjct: 429 EEARKD 434


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.318    0.135    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,441,344
Number of extensions: 64999
Number of successful extensions: 287
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 288
Number of HSP's successfully gapped: 1
Length of query: 431
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 343
Effective length of database: 1,203,190
Effective search space: 412694170
Effective search space used: 412694170
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 132 (55.5 bits)